AFAIK Steam shouldn't cause issues with the majority of mods - however you won't be able to use TDW's .exe patcher to fix the hydrophone or alter the annoying TAI map colours as Steam checks the .exe file at launch.
Steam in general is a very decent platform, however there is one thing - it's often more expensive. At the moment, you can get Silent Hunter 5 for about a fiver on amazon.co.uk - if you buy it on steam you'll pay three times that, even in a Steam sale (was in one recently for £15ish iirc).
If you can go disc for SH5, do.
EDIT: Don't know Macs, sorry Scandiman!